BAHCC1

Summary

BAHCC1 (BAH domain and coiled-coil containing 1, HGNC:29279) is a protein-coding gene on chromosome 17q25.3, encoding BAH and coiled-coil domain-containing protein 1 (Q9P281).

Predicted to enable chromatin binding activity. Predicted to act upstream of or within chromatin organization; locomotory behavior; and neuron differentiation.

Source: NCBI Gene 57597 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_001377448

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29279
Approved symbol	BAHCC1
Name	BAH domain and coiled-coil containing 1
Location	17q25.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1447, BAHD2
Ensembl gene	ENSG00000266074
Ensembl biotype	protein_coding
OMIM	617646
Entrez	57597

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 retained_intron, 2 protein_coding, 1 protein_coding_CDS_not_defined, 1 TEC

ENST00000578541, ENST00000582709, ENST00000583828, ENST00000584330, ENST00000584436, ENST00000585224, ENST00000625166, ENST00000675386

RefSeq mRNA: 2 — MANE Select: NM_001377448 NM_001291324, NM_001377448

CCDS: CCDS74173, CCDS92415

Canonical transcript exons

ENST00000675386 — 28 exons

Exon	Start	End
ENSE00001299770	81456297	81456585
ENSE00001311312	81463611	81466331
ENSE00002694888	81399534	81399917
ENSE00003565014	81457410	81457592
ENSE00003633588	81426800	81426979
ENSE00003711765	81444668	81444826
ENSE00003713751	81444381	81444568
ENSE00003714651	81460866	81462046
ENSE00003716830	81445354	81445681
ENSE00003722883	81445015	81445178
ENSE00003724283	81452723	81452851
ENSE00003730221	81459496	81459604
ENSE00003730777	81455267	81455390
ENSE00003731515	81458813	81458969
ENSE00003732131	81441831	81443564
ENSE00003733183	81438370	81438492
ENSE00003733306	81460277	81460396
ENSE00003733991	81459054	81459168
ENSE00003738895	81460530	81460706
ENSE00003739257	81458621	81458725
ENSE00003741259	81459253	81459328
ENSE00003745576	81462740	81462976
ENSE00003745726	81443809	81443917
ENSE00003745829	81447036	81447848
ENSE00003746114	81451971	81452107
ENSE00003746237	81458165	81458466
ENSE00003749248	81451668	81451870
ENSE00003904583	81395457	81395635

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 95.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.4429 / max 317.1697, expressed in 1553 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
163314	8.2265	1316
163316	1.5671	522
163323	0.7460	342
163324	0.6774	383
163315	0.4603	275
163322	0.4211	189
163328	0.1636	67
163317	0.1575	77
163329	0.0233	7

Top tissues by expression

273 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	95.38	gold quality
cerebellar hemisphere	UBERON:0002245	94.84	gold quality
cerebellar cortex	UBERON:0002129	94.63	gold quality
cerebellum	UBERON:0002037	92.77	gold quality
sural nerve	UBERON:0015488	88.97	gold quality
right frontal lobe	UBERON:0002810	86.62	gold quality
gall bladder	UBERON:0002110	86.61	gold quality
right uterine tube	UBERON:0001302	86.51	gold quality
right coronary artery	UBERON:0001625	85.91	gold quality
right adrenal gland cortex	UBERON:0035827	85.72	gold quality
lower esophagus muscularis layer	UBERON:0035833	85.67	gold quality
lower esophagus	UBERON:0013473	85.60	gold quality
descending thoracic aorta	UBERON:0002345	85.44	gold quality
right lobe of thyroid gland	UBERON:0001119	85.42	gold quality
tendon of biceps brachii	UBERON:0008188	85.22	silver quality
mucosa of stomach	UBERON:0001199	85.10	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.98	gold quality
left uterine tube	UBERON:0001303	84.32	gold quality
right adrenal gland	UBERON:0001233	84.22	gold quality
thoracic aorta	UBERON:0001515	83.97	gold quality
ascending aorta	UBERON:0001496	83.96	gold quality
left adrenal gland cortex	UBERON:0035825	83.85	gold quality
aorta	UBERON:0000947	83.52	gold quality
cartilage tissue	UBERON:0002418	83.45	gold quality
right ovary	UBERON:0002118	83.44	gold quality
tibial artery	UBERON:0007610	83.43	gold quality
apex of heart	UBERON:0002098	83.41	gold quality
popliteal artery	UBERON:0002250	83.41	gold quality
nucleus accumbens	UBERON:0001882	83.34	gold quality
left lobe of thyroid gland	UBERON:0001120	83.26	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

152 targeting BAHCC1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-4728-5P	99.85	69.39	4718

Literature-anchored findings (GeneRIF, showing 2)

• variants. We identified two candidate homozygous missense variants, R942Q in the tubulin-folding cofactor D (TBCD) gene and H250Q in the bromo-adjacent homology domain and coiled-coil containing 1 (BAHCC1) gene, located on chromosome 17q25.3 with an interval of 1.4 Mbp. (PMID:27928163)
• BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis. (PMID:33139953)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	bahcc1b	ENSDARG00000080009
danio_rerio	bahcc1a	ENSDARG00000103739
mus_musculus	Bahcc1	ENSMUSG00000039741
rattus_norvegicus	Bahcc1	ENSRNOG00000043102
drosophila_melanogaster	wge	FBGN0051151

Paralogs (2): BAHD1 (ENSG00000140320), TNRC18 (ENSG00000182095)

Protein

Protein identifiers

BAH and coiled-coil domain-containing protein 1 — Q9P281 (reviewed: Q9P281)

Alternative names: Bromo adjacent homology domain-containing protein 2

All UniProt accessions (2): F8WBW8, Q9P281

RefSeq proteins (2): NP_001278253, NP_001364377* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001025	BAH_dom	Domain
IPR043151	BAH_sf	Homologous_superfamily
IPR047411	Tudor_BAHCC1	Domain
IPR048924	BAHCC1-like_Tudor	Domain
IPR052429	BAH_domain_protein	Family
IPR056841	TNRC18_BAHCC1-like_SH3	Domain

Pfam: PF01426, PF21744, PF24912

UniProt features (45 total): compositionally biased region 19, region of interest 15, sequence variant 6, modified residue 2, chain 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P281-F1	40.51	0.08

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 222, 2274

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 121 (showing top): VALK_AML_WITH_FLT3_ITD, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, HATADA_METHYLATED_IN_LUNG_CANCER_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOMF_CHROMATIN_BINDING, MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, PTEN_DN.V2_DN

GO Biological Process (3): chromatin organization (GO:0006325), locomotory behavior (GO:0007626), neuron differentiation (GO:0030182)

GO Molecular Function (1): chromatin binding (GO:0003682)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular component organization	1
behavior	1
cell differentiation	1
generation of neurons	1
binding	1

Protein interactions and networks

STRING

454 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BAHCC1	IQCE	Q6IPM2	469
BAHCC1	GPAA1	O43292	397
BAHCC1	INTS1	Q8N201	359
BAHCC1	NAV2	Q8IVL1	351
BAHCC1	EFR3B	Q9Y2G0	349
BAHCC1	AGAP2	Q99490	337
BAHCC1	PPP1R35	Q8TAP8	336
BAHCC1	ACCSL	Q4AC99	311
BAHCC1	ASPH	Q12797	310
BAHCC1	PDXDC1	Q6P996	306
BAHCC1	KLHL38	Q2WGJ6	305
BAHCC1	MOSPD1	Q9UJG1	300
BAHCC1	RFX6	Q8HWS3	293
BAHCC1	BAHD1	Q8TBE0	292
BAHCC1	CLEC2B	Q92478	289

IntAct

41 interactions, top by confidence:

A	B	Type	Score
HDAC1	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
RBBP7	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
HDAC1	TNRC18	psi-mi:“MI:0914”(association)	0.790
RBBP4	CDK2AP1	psi-mi:“MI:0914”(association)	0.790
SINHCAF	TNRC18	psi-mi:“MI:0914”(association)	0.640
FOSL2	ZZEF1	psi-mi:“MI:0914”(association)	0.530
FHL2	CNOT1	psi-mi:“MI:0914”(association)	0.530
RBBP4	TNRC18	psi-mi:“MI:0914”(association)	0.530
RBBP7	SMARCA5	psi-mi:“MI:0914”(association)	0.530
RBBP7	EPOP	psi-mi:“MI:0914”(association)	0.530
SAP30	TNRC18	psi-mi:“MI:0914”(association)	0.530
BAHCC1	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
BAHCC1	ATP5IF1	psi-mi:“MI:0915”(physical association)	0.400
CLSTN1	BAHCC1	psi-mi:“MI:0915”(physical association)	0.370
BAHCC1	COMMD1	psi-mi:“MI:0915”(physical association)	0.370
SAP30	BRMS1	psi-mi:“MI:0914”(association)	0.350
HDAC1	TRAK1	psi-mi:“MI:0914”(association)	0.350
ING2	TARSL2	psi-mi:“MI:0914”(association)	0.350
CPNE4	SUPT5H	psi-mi:“MI:0914”(association)	0.350
CPNE7	SUPT5H	psi-mi:“MI:0914”(association)	0.350
MYC		psi-mi:“MI:0914”(association)	0.350
GSTP1	TMSB10	psi-mi:“MI:0914”(association)	0.350
TGIF2LX	TNRC18	psi-mi:“MI:0914”(association)	0.350
ING2	TARS3	psi-mi:“MI:0914”(association)	0.350
SAP30	CLIC2	psi-mi:“MI:0914”(association)	0.350

BioGRID (53): BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-RNA), BAHCC1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-RNA), ATPIF1 (Proximity Label-MS)

ESM2 similar proteins: A2VDR9, A5PKG8, A6NMT0, A7MB40, A8MUI8, E2R9X2, O00257, O15353, O43151, O55187, P19419, P30658, P48382, P52950, P59598, Q03989, Q0GGX2, Q13029, Q14781, Q28BT7, Q2MHN3, Q32MQ0, Q32N19, Q3SWY1, Q3TEI4, Q3U108, Q3UHR0, Q497V6, Q568E2, Q571I4, Q5JPB2, Q5NSW5, Q5TGY3, Q61818, Q6PAL7, Q6ZRI6, Q7TSH3, Q7Z5J4, Q811R2, Q86YN6

Diamond homologs: A2Y0Q2, B8AMA8, B8B8I3, B8BJV8, E6ZGB4, F4JGB7, F4JL28, O75151, P0CF52, P0CH95, P26358, Q08D35, Q12830, Q23541, Q2R837, Q3UHR0, Q3UWM4, Q54DV0, Q5EA28, Q5RHD1, Q5TM48, Q6BER5, Q6P949, Q6ZMT4, Q75IR6, Q7YR48, Q80TJ7, Q84TV4, Q8H383, Q8LA16, Q8S8M9, Q92576, Q9CWW7, Q9FEN9, Q9P0U4, Q9P281, Q9TSV4, Q9UPP1, Q9UT79, Q9W0T1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
HDACs deacetylate histones	6	27.7×	1e-05
NuRD complex assembly	5	27.1×	7e-05
Interaction of NuRD complexes with transcription factors	5	24.4×	8e-05
Potential therapeutics for SARS	5	22.0×	1e-04
NoRC negatively regulates rRNA expression	5	20.1×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of stem cell population maintenance	8	165.6×	3e-14
positive regulation of stem cell population maintenance	8	74.4×	2e-11
negative regulation of transforming growth factor beta receptor signaling pathway	8	37.6×	4e-09
negative regulation of cell migration	8	24.1×	8e-08
chromatin remodeling	5	9.9×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

42 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	12
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

5158 predictions. Top by Δscore:

Variant	Effect	Δscore
17:81441826:CACA:C	acceptor_loss	1.0000
17:81441827:A:AG	acceptor_gain	1.0000
17:81441828:CAGA:C	acceptor_loss	1.0000
17:81441829:A:AG	acceptor_gain	1.0000
17:81441829:AGATA:A	acceptor_loss	1.0000
17:81441830:G:A	acceptor_loss	1.0000
17:81441830:G:GT	acceptor_gain	1.0000
17:81441830:GA:G	acceptor_gain	1.0000
17:81441830:GAT:G	acceptor_gain	1.0000
17:81441830:GATA:G	acceptor_gain	1.0000
17:81441830:GATAA:G	acceptor_gain	1.0000
17:81443918:G:GG	donor_gain	1.0000
17:81451968:CAGGT:C	acceptor_loss	1.0000
17:81451969:A:C	acceptor_loss	1.0000
17:81451970:G:GT	acceptor_loss	1.0000
17:81451970:GGT:G	acceptor_gain	1.0000
17:81452100:GACCA:G	donor_gain	1.0000
17:81452104:A:AG	donor_gain	1.0000
17:81452104:A:G	donor_gain	1.0000
17:81452105:TGA:T	donor_gain	1.0000
17:81452106:GA:G	donor_gain	1.0000
17:81452106:GAG:G	donor_gain	1.0000
17:81452108:G:GG	donor_gain	1.0000
17:81452847:GTCAA:G	donor_gain	1.0000
17:81452852:G:GG	donor_gain	1.0000
17:81457574:G:GT	donor_gain	1.0000
17:81457575:A:T	donor_gain	1.0000
17:81457580:C:T	donor_gain	1.0000
17:81457585:GTTGC:G	donor_gain	1.0000
17:81457586:TTGCT:T	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000042484 (17:81427815 G>A,T), RS1000051684 (17:81456216 A>C), RS1000150156 (17:81439474 G>A), RS1000172139 (17:81431877 G>T), RS1000218577 (17:81402468 T>C), RS1000266745 (17:81406693 C>A,G,T), RS1000273699 (17:81464096 G>A,T), RS1000435005 (17:81427667 C>T), RS1000451677 (17:81430690 G>A), RS1000481652 (17:81441478 T>A,C,G), RS1000569156 (17:81402306 C>T), RS1000579354 (17:81463033 C>T), RS1000607299 (17:81405581 G>A), RS1000677910 (17:81405313 A>G), RS1000786638 (17:81409750 C>T)

Disease associations

OMIM: gene MIM:617646 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST004034_5	Temporomandibular joint disorder	3.000000e-08
GCST006288_298	Heel bone mineral density	6.000000e-10
GCST006288_65	Heel bone mineral density	4.000000e-06
GCST006586_39	Urinary albumin excretion	1.000000e-09
GCST006979_258	Heel bone mineral density	2.000000e-18
GCST007323_49	Risk-taking tendency (4-domain principal component model)	4.000000e-08
GCST007328_80	Alcohol consumption (drinks per week)	1.000000e-08
GCST008258_20	Alcohol use disorder (consumption score)	8.000000e-10
GCST008258_6	Alcohol use disorder (consumption score)	5.000000e-09
GCST008295_28	Number of decayed, missing and filled tooth surfaces or use of dentures	7.000000e-09
GCST008306_15	Dentures	1.000000e-08
GCST008522_68	Bitter alcoholic beverage consumption	2.000000e-06
GCST008794_6	Urinary albumin-to-creatinine ratio	3.000000e-08
GCST009640_52	Urinary albumin-to-creatinine ratio	9.000000e-09
GCST010002_133	Refractive error	2.000000e-50
GCST010774_25	Essential hypertension (time to event)	2.000000e-08
GCST90000025_622	Appendicular lean mass	7.000000e-23

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density
EFO:0004285	albuminuria
EFO:0008579	risk-taking behaviour
EFO:0007645	longitudinal alcohol consumption measurement
EFO:0009458	alcohol use disorder measurement
EFO:0010078	dentures
EFO:0010092	bitter alcoholic beverage consumption measurement
EFO:0007778	urinary albumin to creatinine ratio
EFO:0004918	age at diagnosis
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Cisplatin	decreases expression	2
Tretinoin	decreases expression	2
Valproic Acid	decreases expression, increases methylation	2
Particulate Matter	increases expression, increases abundance	2
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases methylation, affects cotreatment	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
ferrous chloride	decreases expression	1
abrine	increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	affects expression, increases abundance	1
Vehicle Emissions	increases abundance, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	decreases expression	1
Hydrogen Peroxide	affects expression	1
Ozone	increases abundance, affects expression	1
Smoke	decreases expression	1
Dronabinol	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.